Импорт phyloseq объекта и библиотек
Датасет - хроносерия разложения соломы - от фактор Day 10ти уровней
library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(ANCOMBC)
library(heatmaply)
library(compositions)
library(igraph)
library(WGCNA)
require(DESeq2)
require(phyloseq)
ps.f <- readRDS("psf2")
#phyloseq object to ampvis2 object
#https://gist.github.com/KasperSkytte/8d0ca4206a66be7ff6d76fc4ab8e66c6
phyloseq_to_ampvis2 <- function(physeq) {
#check object for class
if(!any(class(physeq) %in% "phyloseq"))
stop("physeq object must be of class \"phyloseq\"", call. = FALSE)
#ampvis2 requires taxonomy and abundance table, phyloseq checks for the latter
if(is.null(physeq@tax_table))
stop("No taxonomy found in the phyloseq object and is required for ampvis2", call. = FALSE)
#OTUs must be in rows, not columns
if(phyloseq::taxa_are_rows(physeq))
abund <- as.data.frame(phyloseq::otu_table(physeq)@.Data)
else
abund <- as.data.frame(t(phyloseq::otu_table(physeq)@.Data))
#tax_table is assumed to have OTUs in rows too
tax <- phyloseq::tax_table(physeq)@.Data
#merge by rownames (OTUs)
otutable <- merge(
abund,
tax,
by = 0,
all.x = TRUE,
all.y = FALSE,
sort = FALSE
)
colnames(otutable)[1] <- "OTU"
#extract sample_data (metadata)
if(!is.null(physeq@sam_data)) {
metadata <- data.frame(
phyloseq::sample_data(physeq),
row.names = phyloseq::sample_names(physeq),
stringsAsFactors = FALSE,
check.names = FALSE
)
#check if any columns match exactly with rownames
#if none matched assume row names are sample identifiers
samplesCol <- unlist(lapply(metadata, function(x) {
identical(x, rownames(metadata))}))
if(any(samplesCol)) {
#error if a column matched and it's not the first
if(!samplesCol[[1]])
stop("Sample ID's must be in the first column in the sample metadata, please reorder", call. = FALSE)
} else {
#assume rownames are sample identifiers, merge at the end with name "SampleID"
if(any(colnames(metadata) %in% "SampleID"))
stop("A column in the sample metadata is already named \"SampleID\" but does not seem to contain sample ID's", call. = FALSE)
metadata$SampleID <- rownames(metadata)
#reorder columns so SampleID is the first
metadata <- metadata[, c(which(colnames(metadata) %in% "SampleID"), 1:(ncol(metadata)-1L)), drop = FALSE]
}
} else
metadata <- NULL
#extract phylogenetic tree, assumed to be of class "phylo"
if(!is.null(physeq@phy_tree)) {
tree <- phyloseq::phy_tree(physeq)
} else
tree <- NULL
#extract OTU DNA sequences, assumed to be of class "XStringSet"
if(!is.null(physeq@refseq)) {
#convert XStringSet to DNAbin using a temporary file (easiest)
fastaTempFile <- tempfile(pattern = "ampvis2_", fileext = ".fa")
Biostrings::writeXStringSet(physeq@refseq, filepath = fastaTempFile)
} else
fastaTempFile <- NULL
#load as normally with amp_load
ampvis2::amp_load(
otutable = otutable,
metadata = metadata,
tree = tree,
fasta = fastaTempFile
)
}
#variance stabilisation from DESeq2
ps_vst <- function(ps, factor){
diagdds = phyloseq_to_deseq2(ps, as.formula(paste( "~", factor)))
diagdds = estimateSizeFactors(diagdds, type="poscounts")
diagdds = estimateDispersions(diagdds, fitType = "local")
pst <- varianceStabilizingTransformation(diagdds)
pst.dimmed <- t(as.matrix(assay(pst)))
# pst.dimmed[pst.dimmed < 0.0] <- 0.0
ps.varstab <- ps
otu_table(ps.varstab) <- otu_table(pst.dimmed, taxa_are_rows = FALSE)
return(ps.varstab)
}
#WGCNA visualisation
#result - list class object with attributes:
# ps - phyloseq object
# amp - ampwis2 object
# heat - heatmap with absalute read numbers
# heat_rel - hetmap with relative abundances
# tree - phylogenetic tree with taxonomy
color_filt <- function(ps, df){
library(tidyverse)
library(reshape2)
library(gridExtra)
l = list()
for (i in levels(df$module)){
message(i)
color_name <- df %>%
filter(module == i) %>%
pull(asv) %>%
unique()
ps.col <- prune_taxa(color_name, ps)
amp.col <- phyloseq_to_ampvis2(ps.col)
heat <- amp_heatmap(amp.col, tax_show = 60,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
normalise=FALSE,
showRemainingTaxa = TRUE)
ps.rel <- phyloseq::transform_sample_counts(ps.col, function(x) x / sum(x) * 100)
amp.r <- phyloseq_to_ampvis2(ps.rel)
heat.rel <- amp_heatmap(amp.r, tax_show = 60,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
normalise=FALSE,
showRemainingTaxa = TRUE)
tree <- ps.col@phy_tree
taxa <- as.data.frame(ps.col@tax_table@.Data)
p1 <- ggtree(tree) +
geom_tiplab(size=2, align=TRUE, linesize=.5) +
theme_tree2()
taxa[taxa == "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"] <- "Allorhizobium"
taxa[taxa == "Burkholderia-Caballeronia-Paraburkholderia"] <- "Burkholderia"
tx <- taxa %>%
rownames_to_column("id") %>%
mutate(id = factor(id, levels = rev(get_taxa_name(p1)))) %>%
dplyr::select(-c(Kingdom, Species, Order)) %>%
melt(id.var = 'id')
p2 <- ggplot(tx, aes(variable, id)) +
geom_tile(aes(fill = value), alpha = 0.4) +
geom_text(aes(label = value), size = 3) +
theme_bw() +
theme(legend.position = "none",
axis.ticks.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank())
p <- ggpubr::ggarrange(p1, p2, widths = c(0.9, 1))
l[[i]] <- list("ps" = ps.col,
"amp" = amp.col,
"heat" = heat,
"heat_rel" = heat.rel,
"tree" = p,
"taxa" = knitr::kable(taxa))
}
return(l)
}
detachAllPackages <- function() {
basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")
package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]
package.list <- setdiff(package.list,basic.packages)
if (length(package.list)>0) for (package in package.list) detach(package, character.only=TRUE, force = TRUE)
}
Разделим датасет на две группы
1-я - в более чем 10% образцов должно быть хотя бы 10 ридов - эта группа пойдет в анализ далее
ps.inall <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) > (0.1*length(x)), TRUE)
amp.inall <- phyloseq_to_ampvis2(ps.inall)
amp_heatmap(amp.inall,
tax_show = 40,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
normalise=FALSE,
showRemainingTaxa = TRUE)
Вторая - оставшиеся, но более 100 ридов по всем образцам(далее -
вылетающие мажоры(ВМ))
Остальные филотипы выкидываем из анализа
ps.exl <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) < (0.1*length(x)), TRUE)
ps.exl <- prune_taxa(taxa_sums(ps.exl) > 100, ps.exl)
amp.exl <- phyloseq_to_ampvis2(ps.exl)
amp_heatmap(amp.exl,
tax_show = 40,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
normalise=FALSE,
showRemainingTaxa = TRUE)
То же, но c относительной представленностью.
ps.per <- phyloseq::transform_sample_counts(ps.f, function(x) x / sum(x) * 100)
ps.exl.taxa <- taxa_names(ps.exl)
ps.per.exl <- prune_taxa(ps.exl.taxa, ps.per)
amp.exl.r <- phyloseq_to_ampvis2(ps.per.exl)
amp_heatmap(amp.exl.r, tax_show = 60,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
round = 2,
normalise=FALSE,
showRemainingTaxa = TRUE)
amp_heatmap(amp.exl.r, tax_show = 60,
group_by = "Day",
tax_aggregate = "OTU",
tax_add = "Genus",
round = 2,
normalise=FALSE, )
ВМ объединенные по родам. Относительная представленность.
amp_heatmap(amp.exl.r,
tax_show = 30,
group_by = "Day",
tax_aggregate = "Genus",
tax_add = "Phylum",
tax_class = "Proteobacteria",
round = 2,
normalise=FALSE,
showRemainingTaxa = TRUE)
Если посмотреть, если как распределяются ВМ по дням - похоже распределение ВМ связано не только с особенностью отдельных мешочков, но и с чисто техническими особенностями - вылетающие значения вылетают в основном не с биологическими повторностями, а с техническими(красная линия)
p_box <- phyloseq::sample_sums(ps.per.exl) %>%
as.data.frame(col.names = "values") %>%
setNames(., nm = "values") %>%
rownames_to_column("samples") %>%
mutate(Day = sapply(strsplit(samples, "-"), `[`, 3)) %>%
ggplot(aes(x=Day, y=values, color=Day, fill = Day)) +
geom_boxplot(aes(color=Day, fill = Day)) +
geom_point(color = "black", position = position_dodge(width=0.2)) +
geom_hline(yintercept = 10, colour = "red") +
theme_bw() +
theme(legend.position = "none")
p_box <- p_box + viridis::scale_color_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.5)
p_box + viridis::scale_fill_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.3)
после clr нормализации
otu.inall <- as.data.frame(ps.inall@otu_table@.Data)
ps.inall.clr <- ps.inall
otu_table(ps.inall.clr) <- phyloseq::otu_table(compositions::clr(otu.inall), taxa_are_rows = FALSE)
data <- ps.inall.clr@otu_table@.Data %>%
as.data.frame()
rownames(data) <- as.character(ps.inall.clr@sam_data$Description)
powers <- c(c(1:10), seq(from = 12, to=30, by=1))
sft <- pickSoftThreshold(data, powerVector = powers, verbose = 5, networkType = "signed")
## pickSoftThreshold: will use block size 338.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 338 of 338
## Warning: executing %dopar% sequentially: no parallel backend registered
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.185 23.60 0.8790 168.0000 168.00000 172.000
## 2 2 0.199 -15.50 0.8970 87.6000 87.20000 95.100
## 3 3 0.518 -13.10 0.8580 47.3000 46.80000 55.900
## 4 4 0.390 -6.46 0.8050 26.5000 26.00000 34.500
## 5 5 0.262 -3.46 0.7820 15.4000 14.90000 22.300
## 6 6 0.232 -2.30 0.7770 9.2300 8.78000 15.000
## 7 7 0.251 -1.87 0.6990 5.7300 5.36000 10.500
## 8 8 0.319 -1.75 0.7570 3.6800 3.41000 7.620
## 9 9 0.527 -2.07 0.7770 2.4400 2.20000 5.890
## 10 10 0.648 -2.28 0.8490 1.6600 1.47000 4.690
## 11 12 0.827 -2.41 0.8970 0.8420 0.69300 3.190
## 12 13 0.793 -2.38 0.7930 0.6220 0.49000 2.700
## 13 14 0.277 -3.97 0.0914 0.4690 0.35500 2.320
## 14 15 0.282 -3.83 0.1000 0.3610 0.26100 2.010
## 15 16 0.894 -2.17 0.9030 0.2820 0.19800 1.770
## 16 17 0.905 -2.10 0.9080 0.2240 0.15000 1.560
## 17 18 0.922 -2.04 0.9240 0.1810 0.11500 1.390
## 18 19 0.927 -2.01 0.9230 0.1480 0.08820 1.250
## 19 20 0.938 -1.93 0.9370 0.1220 0.06780 1.130
## 20 21 0.946 -1.86 0.9470 0.1020 0.05260 1.020
## 21 22 0.315 -3.12 0.2220 0.0856 0.04140 0.926
## 22 23 0.303 -3.96 0.1560 0.0728 0.03270 0.844
## 23 24 0.307 -2.92 0.1940 0.0623 0.02590 0.772
## 24 25 0.303 -2.84 0.1800 0.0538 0.02060 0.708
## 25 26 0.921 -1.63 0.8990 0.0467 0.01650 0.657
## 26 27 0.892 -1.61 0.8650 0.0408 0.01320 0.622
## 27 28 0.155 -1.93 -0.0202 0.0359 0.01040 0.591
## 28 29 0.199 -2.77 -0.0228 0.0317 0.00841 0.563
## 29 30 0.199 -2.69 -0.0203 0.0282 0.00684 0.537
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")
после vst нормализации
ps.varstab <- ps_vst(ps.inall, "Day")
data2 <- ps.varstab@otu_table@.Data %>%
as.data.frame()
rownames(data2) <- as.character(ps.varstab@sam_data$Description)
powers <- c(seq(from = 1, to=10, by=0.5), seq(from = 11, to=20, by=1))
sft2 <- pickSoftThreshold(data2, powerVector = powers, verbose = 5, networkType = "signed hybrid")
## pickSoftThreshold: will use block size 338.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 338 of 338
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1.0 0.409 -1.05 0.704 50.100 45.60000 97.80
## 2 1.5 0.578 -1.07 0.895 30.900 27.00000 71.20
## 3 2.0 0.723 -1.15 0.942 20.300 17.90000 53.60
## 4 2.5 0.767 -1.24 0.871 14.000 12.00000 41.70
## 5 3.0 0.809 -1.31 0.909 10.000 7.86000 33.40
## 6 3.5 0.872 -1.31 0.958 7.380 5.39000 27.30
## 7 4.0 0.888 -1.30 0.968 5.580 3.76000 22.60
## 8 4.5 0.858 -1.36 0.910 4.320 2.67000 19.00
## 9 5.0 0.892 -1.36 0.943 3.400 1.94000 16.20
## 10 5.5 0.899 -1.38 0.954 2.720 1.41000 13.90
## 11 6.0 0.896 -1.39 0.962 2.210 1.07000 12.10
## 12 6.5 0.897 -1.33 0.962 1.820 0.84700 10.60
## 13 7.0 0.910 -1.30 0.970 1.520 0.65400 9.30
## 14 7.5 0.914 -1.31 0.966 1.280 0.51500 8.25
## 15 8.0 0.913 -1.28 0.954 1.090 0.41500 7.36
## 16 8.5 0.905 -1.28 0.937 0.938 0.34000 6.59
## 17 9.0 0.895 -1.30 0.913 0.813 0.27800 5.99
## 18 9.5 0.878 -1.33 0.900 0.709 0.23200 5.49
## 19 10.0 0.886 -1.34 0.894 0.624 0.19100 5.07
## 20 11.0 0.911 -1.31 0.928 0.491 0.12500 4.35
## 21 12.0 0.890 -1.29 0.894 0.396 0.08590 3.79
## 22 13.0 0.910 -1.26 0.918 0.325 0.06120 3.33
## 23 14.0 0.882 -1.25 0.856 0.272 0.04420 2.95
## 24 15.0 0.889 -1.19 0.864 0.230 0.03230 2.63
## 25 16.0 0.913 -1.18 0.893 0.198 0.02240 2.35
## 26 17.0 0.930 -1.16 0.912 0.172 0.01620 2.20
## 27 18.0 0.955 -1.19 0.947 0.151 0.01190 2.09
## 28 19.0 0.908 -1.21 0.896 0.134 0.00896 1.99
## 29 20.0 0.916 -1.21 0.906 0.120 0.00649 1.91
plot(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")
detachAllPackages()
library(WGCNA)
net3 <- WGCNA::blockwiseModules(data2,
power=5.5,
TOMType="signed",
networkType="signed hybrid",
nThreads=0)
mergedColors2 <- WGCNA::labels2colors(net3$colors, colorSeq = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))
plotDendroAndColors(
net3$dendrograms[[1]],
mergedColors2[net3$blockGenes[[1]]],
"Module colors",
dendroLabels = FALSE,
hang = 0.03,
addGuide = TRUE,
guideHang = 0.05)
library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(heatmaply)
library(WGCNA)
library(phyloseq)
library(ggtree)
library(tidyverse)
modules_of_interest = mergedColors2 %>%
unique()
module_df <- data.frame(
asv = names(net3$colors),
colors = mergedColors2
)
# module_df[module_df == "yellow"] <- "salmon"
submod <- module_df %>%
subset(colors %in% modules_of_interest)
row.names(module_df) = module_df$asv
subexpr = as.data.frame(t(data2))[submod$asv,]
submod_df <- data.frame(subexpr) %>%
mutate(
asv = row.names(.)
) %>%
pivot_longer(-asv) %>%
mutate(
module = module_df[asv,]$colors
)
submod_df <- submod_df %>%
mutate(name = gsub("\\_.*","",submod_df$name)) %>%
group_by(name, asv) %>%
summarise(value = mean(value), asv = asv, module = module) %>%
relocate(c(asv, name, value, module)) %>%
ungroup() %>%
mutate(module = as.factor(module))
p <- submod_df %>%
ggplot(., aes(x=name, y=value, group=asv)) +
geom_line(aes(color = module),
alpha = 0.2) +
theme_bw() +
theme(
axis.text.x = element_text(angle = 90),
legend.position = "none") +
facet_grid(rows = vars(module)) +
labs(x = "treatment",
y = "normalized expression")
p + scale_color_manual(values = levels(submod_df$module))
ps.inall.col <- ps.inall
df <- module_df %>%
rename("id" = "asv")
df <- df %>%
dplyr::select(-"id") %>%
mutate(colors = as.factor(colors))
taxa <- as.data.frame(ps.inall@tax_table@.Data)
tx <- cbind(taxa, df)
tx$colors <- factor(tx$colors, levels = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))
tax_table(ps.inall.col) <- tax_table(as.matrix(tx))
ord <- ordinate(ps.inall.col, "NMDS", "unifrac")
## Run 0 stress 0.0685455
## Run 1 stress 0.05568715
## ... New best solution
## ... Procrustes: rmse 0.04076815 max resid 0.2160842
## Run 2 stress 0.05628488
## Run 3 stress 0.05568714
## ... New best solution
## ... Procrustes: rmse 0.0001464974 max resid 0.0005071635
## ... Similar to previous best
## Run 4 stress 0.05568713
## ... New best solution
## ... Procrustes: rmse 0.000007985248 max resid 0.00002963397
## ... Similar to previous best
## Run 5 stress 0.06728204
## Run 6 stress 0.07544621
## Run 7 stress 0.05628486
## Run 8 stress 0.3904836
## Run 9 stress 0.07544606
## Run 10 stress 0.0556871
## ... New best solution
## ... Procrustes: rmse 0.00009004597 max resid 0.0003095288
## ... Similar to previous best
## Run 11 stress 0.0556871
## ... Procrustes: rmse 0.00001239394 max resid 0.00006280792
## ... Similar to previous best
## Run 12 stress 0.05628495
## Run 13 stress 0.05568712
## ... Procrustes: rmse 0.00003561188 max resid 0.0001044555
## ... Similar to previous best
## Run 14 stress 0.07803506
## Run 15 stress 0.06774709
## Run 16 stress 0.07544601
## Run 17 stress 0.05568711
## ... Procrustes: rmse 0.00002025967 max resid 0.00007269349
## ... Similar to previous best
## Run 18 stress 0.07911206
## Run 19 stress 0.07973318
## Run 20 stress 0.067282
## *** Solution reached
plot_ordination(ps.inall.col, ord, type = "species", color = "colors") +
scale_color_manual(values = c("salmon", "darkgreen", "cyan", "red", "blue", "plum")) +
theme_bw() +
theme(legend.position = "none")
Далее идут одинаковые картинки по всем группам.
l_vst <- color_filt(ps.inall, submod_df)
l_vst
$blue \(blue\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 86 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 86 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 86 tips and 85 internal nodes ] refseq() DNAStringSet: [ 86 reference sequences ]
\(blue\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 86 89493 0 11387 1819 Avg#Reads 2556.94
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 86(100%) 86(100%) 86(100%) 85(98.84%) 79(91.86%) 50(58.14%) 7(8.14%)
Metadata variables: 3 SampleID, Day, Description
\(blue\)heat
\(blue\)heat_rel
\(blue\)tree
\(blue\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq314 | Bacteria | Cyanobacteria | Vampirivibrionia | Obscuribacterales | Obscuribacteraceae | NA | NA |
| Seq23 | Bacteria | Cyanobacteria | Vampirivibrionia | Obscuribacterales | Obscuribacteraceae | NA | NA |
| Seq65 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingomonas | NA |
| Seq188 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | soli |
| Seq334 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | NA |
| Seq75 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | NA |
| Seq167 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | massiliensis |
| Seq273 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Kaistiaceae | Kaistia | NA |
| Seq131 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Pseudolabrys | NA |
| Seq138 | Bacteria | Proteobacteria | Alphaproteobacteria | Micropepsales | Micropepsaceae | NA | NA |
| Seq104 | Bacteria | Proteobacteria | Alphaproteobacteria | Micropepsales | Micropepsaceae | NA | NA |
| Seq129 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Altererythrobacter | NA |
| Seq28 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Devosiaceae | Devosia | NA |
| Seq360 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Mesorhizobium | NA |
| Seq292 | Bacteria | Proteobacteria | Alphaproteobacteria | Caulobacterales | Caulobacteraceae | NA | NA |
| Seq166 | Bacteria | Proteobacteria | Alphaproteobacteria | Caulobacterales | Hyphomonadaceae | Hirschia | NA |
| Seq39 | Bacteria | Gemmatimonadota | Gemmatimonadetes | Gemmatimonadales | Gemmatimonadaceae | NA | NA |
| Seq30 | Bacteria | Actinobacteriota | Thermoleophilia | Solirubrobacterales | Solirubrobacteraceae | Conexibacter | NA |
| Seq151 | Bacteria | Actinobacteriota | Thermoleophilia | Solirubrobacterales | 67-14 | NA | NA |
| Seq250 | Bacteria | Actinobacteriota | Thermoleophilia | Solirubrobacterales | 67-14 | NA | NA |
| Seq135 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq46 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq35 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq106 | Bacteria | Myxococcota | Polyangia | Polyangiales | Sandaracinaceae | NA | NA |
| Seq345 | Bacteria | Bdellovibrionota | Oligoflexia | 0319-6G20 | NA | NA | NA |
| Seq198 | Bacteria | Bdellovibrionota | Bdellovibrionia | Bdellovibrionales | Bdellovibrionaceae | Bdellovibrio | NA |
| Seq97 | Bacteria | Bdellovibrionota | Bdellovibrionia | Bdellovibrionales | Bdellovibrionaceae | Bdellovibrio | NA |
| Seq183 | Bacteria | Dependentiae | Babeliae | Babeliales | UBA12409 | NA | NA |
| Seq424 | Bacteria | Actinobacteriota | Actinobacteria | Propionibacteriales | Nocardioidaceae | Kribbella | NA |
| Seq136 | Bacteria | Actinobacteriota | Acidimicrobiia | Microtrichales | Iamiaceae | Iamia | NA |
| Seq174 | Bacteria | Actinobacteriota | Acidimicrobiia | Microtrichales | Iamiaceae | Iamia | NA |
| Seq43 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | Galbitalea | NA |
| Seq420 | Bacteria | Actinobacteriota | Actinobacteria | Micromonosporales | Micromonosporaceae | Luedemannella | NA |
| Seq127 | Bacteria | Actinobacteriota | Actinobacteria | Micromonosporales | Micromonosporaceae | Dactylosporangium | NA |
| Seq288 | Bacteria | Actinobacteriota | Actinobacteria | Streptomycetales | Streptomycetaceae | NA | NA |
| Seq449 | Bacteria | Actinobacteriota | Actinobacteria | Propionibacteriales | Propionibacteriaceae | Jiangella | NA |
| Seq91 | Bacteria | Bacteroidota | Bacteroidia | Bacteroidales | NA | NA | NA |
| Seq149 | Bacteria | Bacteroidota | Bacteroidia | Bacteroidetes VC2.1 Bac22 | NA | NA | NA |
| Seq169 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | Sphingobacteriaceae | Mucilaginibacter | calamicampi |
| Seq81 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | NS11-12 marine group | NA | NA |
| Seq211 | Bacteria | Bacteroidota | Bacteroidia | NA | NA | NA | NA |
| Seq119 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | env.OPS 17 | NA | NA |
| Seq77 | Bacteria | Spirochaetota | Spirochaetia | Spirochaetales | Spirochaetaceae | Salinispira | NA |
| Seq175 | Bacteria | Spirochaetota | Spirochaetia | Spirochaetales | Spirochaetaceae | Spirochaeta 2 | NA |
| Seq305 | Bacteria | Chloroflexi | Anaerolineae | Anaerolineales | Anaerolineaceae | NA | NA |
| Seq379 | Bacteria | Chloroflexi | Chloroflexia | Chloroflexales | Roseiflexaceae | NA | NA |
| Seq165 | Bacteria | Chloroflexi | Chloroflexia | Chloroflexales | Roseiflexaceae | NA | NA |
| Seq327 | Bacteria | Chloroflexi | Chloroflexia | Thermomicrobiales | JG30-KF-CM45 | NA | NA |
| Seq252 | Bacteria | Armatimonadota | Fimbriimonadia | Fimbriimonadales | Fimbriimonadaceae | NA | NA |
| Seq382 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Pedosphaerales | Pedosphaeraceae | NA | NA |
| Seq123 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Opitutales | Opitutaceae | Lacunisphaera | limnophila |
| Seq124 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Terrimicrobiaceae | Terrimicrobium | NA |
| Seq325 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Chthoniobacteraceae | LD29 | NA |
| Seq272 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Verrucomicrobiales | Verrucomicrobiaceae | Roseimicrobium | gellanilyticum |
| Seq402 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Verrucomicrobiales | Rubritaleaceae | Luteolibacter | NA |
| Seq322 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | NA | NA |
| Seq356 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | NA | NA |
| Seq259 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | Pir4 lineage | NA |
| Seq279 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | Pir4 lineage | NA |
| Seq214 | Bacteria | Planctomycetota | Planctomycetes | Planctomycetales | Rubinisphaeraceae | SH-PL14 | NA |
| Seq209 | Bacteria | Planctomycetota | Planctomycetes | Planctomycetales | Schlesneriaceae | Schlesneria | NA |
| Seq229 | Bacteria | Acidobacteriota | Vicinamibacteria | Vicinamibacterales | Vicinamibacteraceae | NA | NA |
| Seq275 | Bacteria | Acidobacteriota | Vicinamibacteria | Vicinamibacterales | Vicinamibacteraceae | NA | NA |
| Seq247 | Bacteria | Acidobacteriota | Vicinamibacteria | Vicinamibacterales | NA | NA | NA |
| Seq316 | Bacteria | Bacteroidota | Kapabacteria | Kapabacteriales | NA | NA | NA |
| Seq371 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq12 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq153 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq326 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq10 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | NA | NA |
| Seq82 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Terrimonas | NA |
| Seq462 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Pseudoflavitalea | NA |
| Seq150 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Flavitalea | NA |
| Seq290 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Edaphobaculum | NA |
| Seq339 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Edaphobaculum | NA |
| Seq120 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Taibaiella | NA |
| Seq233 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | 211ds20 | NA | NA |
| Seq133 | Bacteria | Proteobacteria | Gammaproteobacteria | Steroidobacterales | Steroidobacteraceae | Steroidobacter | flavus |
| Seq349 | Bacteria | Proteobacteria | Gammaproteobacteria | Steroidobacterales | Steroidobacteraceae | Steroidobacter | NA |
| Seq315 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq57 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq96 | Bacteria | Proteobacteria | Gammaproteobacteria | R7C24 | NA | NA | NA |
| Seq170 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq94 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Rhodanobacteraceae | Dokdonella | ginsengisoli |
| Seq114 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | NA | NA |
| Seq235 | Bacteria | Proteobacteria | Gammaproteobacteria | Legionellales | Legionellaceae | Legionella | NA |
$cyan \(cyan\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]
\(cyan\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 176073 336 15108 4911 Avg#Reads 5030.66
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 30(100%) 29(96.67%) 2(6.67%)
Metadata variables: 3 SampleID, Day, Description
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\(cyan\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq98 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Burkholderiaceae | Burkholderia | telluris |
| Seq64 | Bacteria | Proteobacteria | Alphaproteobacteria | Azospirillales | Inquilinaceae | Inquilinus | ginsengisoli |
| Seq4 | Bacteria | Proteobacteria | Alphaproteobacteria | Azospirillales | Inquilinaceae | Inquilinus | NA |
| Seq244 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Pseudorhodoplanes | NA |
| Seq11 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Bradyrhizobium | NA |
| Seq74 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Bradyrhizobium | NA |
| Seq22 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Starkeya | NA |
| Seq45 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Allorhizobium | NA |
| Seq9 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Allorhizobium | NA |
| Seq29 | Bacteria | Myxococcota | Polyangia | Nannocystales | Nannocystaceae | Nannocystis | NA |
| Seq239 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Labilithrix | NA |
| Seq50 | Bacteria | Actinobacteriota | Actinobacteria | Corynebacteriales | Mycobacteriaceae | Mycobacterium | NA |
| Seq34 | Bacteria | Actinobacteriota | Actinobacteria | Streptosporangiales | Streptosporangiaceae | Herbidospora | NA |
| Seq56 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq25 | Bacteria | Firmicutes | Bacilli | Bacillales | Bacillaceae | Terribacillus | NA |
| Seq3 | Bacteria | Firmicutes | Bacilli | Bacillales | Bacillaceae | Bacillus | NA |
| Seq5 | Bacteria | Firmicutes | Bacilli | Bacillales | Bacillaceae | Bacillus | NA |
| Seq13 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | NA | NA |
| Seq7 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Solibacillus | NA |
| Seq19 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Solibacillus | NA |
| Seq17 | Bacteria | Planctomycetota | Planctomycetes | Isosphaerales | Isosphaeraceae | Singulisphaera | NA |
| Seq324 | Bacteria | Acidobacteriota | Acidobacteriae | Acidobacteriales | Acidobacteriaceae (Subgroup 1) | Edaphobacter | NA |
| Seq16 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq6 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq1 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq109 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq49 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Taibaiella | NA |
| Seq73 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Spirosomaceae | Dyadobacter | NA |
| Seq15 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Rhodanobacteraceae | Luteibacter | NA |
| Seq26 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Luteimonas | NA |
$darkgreen \(darkgreen\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 44 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 44 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 44 tips and 43 internal nodes ] refseq() DNAStringSet: [ 44 reference sequences ]
\(darkgreen\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 44 12360 0 2468 65 Avg#Reads 353.14
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 44(100%) 44(100%) 44(100%) 43(97.73%) 40(90.91%) 24(54.55%) 3(6.82%)
Metadata variables: 3 SampleID, Day, Description
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\(darkgreen\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq342 | Archaea | Crenarchaeota | Nitrososphaeria | Nitrososphaerales | Nitrososphaeraceae | NA | NA |
| Seq196 | Archaea | Crenarchaeota | Nitrososphaeria | Nitrososphaerales | Nitrososphaeraceae | Candidatus Nitrocosmicus | NA |
| Seq276 | Archaea | Crenarchaeota | Nitrososphaeria | Nitrososphaerales | Nitrososphaeraceae | NA | NA |
| Seq419 | Archaea | Crenarchaeota | Nitrososphaeria | Nitrososphaerales | Nitrososphaeraceae | NA | NA |
| Seq454 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | Aquicella | NA |
| Seq329 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingomonas | jaspsi |
| Seq332 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhodospirillales | Magnetospiraceae | NA | NA |
| Seq429 | Bacteria | Proteobacteria | Alphaproteobacteria | Acetobacterales | Acetobacteraceae | NA | NA |
| Seq195 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Pseudorhodoplanes | NA |
| Seq144 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Pseudolabrys | NA |
| Seq369 | Bacteria | Proteobacteria | Alphaproteobacteria | Micropepsales | Micropepsaceae | NA | NA |
| Seq362 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Altererythrobacter | NA |
| Seq428 | Bacteria | Proteobacteria | Alphaproteobacteria | Caulobacterales | Caulobacteraceae | Phenylobacterium | NA |
| Seq347 | Bacteria | Nitrospirota | Nitrospiria | Nitrospirales | Nitrospiraceae | Nitrospira | japonica |
| Seq328 | Bacteria | Myxococcota | Polyangia | Haliangiales | Haliangiaceae | Haliangium | NA |
| Seq348 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq308 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq256 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Minicystis | NA |
| Seq302 | Bacteria | Bdellovibrionota | Oligoflexia | 0319-6G20 | NA | NA | NA |
| Seq435 | Bacteria | Actinobacteriota | Actinobacteria | Propionibacteriales | Propionibacteriaceae | Microlunatus | NA |
| Seq291 | Bacteria | Actinobacteriota | Acidimicrobiia | IMCC26256 | NA | NA | NA |
| Seq392 | Bacteria | Actinobacteriota | Acidimicrobiia | Microtrichales | Ilumatobacteraceae | NA | NA |
| Seq321 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | NS11-12 marine group | NA | NA |
| Seq186 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq204 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Paenisporosarcina | NA |
| Seq146 | Bacteria | Spirochaetota | Spirochaetia | Spirochaetales | Spirochaetaceae | Spirochaeta 2 | NA |
| Seq359 | Bacteria | Patescibacteria | Saccharimonadia | Saccharimonadales | LWQ8 | NA | NA |
| Seq269 | Bacteria | Chloroflexi | Chloroflexia | Chloroflexales | Roseiflexaceae | NA | NA |
| Seq267 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Opitutales | Opitutaceae | Lacunisphaera | NA |
| Seq320 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Opitutales | Opitutaceae | Opitutus | NA |
| Seq203 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Terrimicrobiaceae | Terrimicrobium | NA |
| Seq497 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | NA | NA |
| Seq384 | Bacteria | Planctomycetota | Planctomycetes | Planctomycetales | NA | NA | NA |
| Seq155 | Bacteria | Acidobacteriota | Blastocatellia | Blastocatellales | Blastocatellaceae | NA | NA |
| Seq350 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | env.OPS 17 | NA | NA |
| Seq224 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Terrimonas | NA |
| Seq409 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Edaphobaculum | NA |
| Seq337 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Taibaiella | NA |
| Seq494 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Amoebophilaceae | Candidatus Amoebophilus | NA |
| Seq277 | Bacteria | Proteobacteria | Gammaproteobacteria | NA | NA | NA | NA |
| Seq191 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq335 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Luteimonas | vadosa |
| Seq157 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Rhodanobacteraceae | Dokdonella | NA |
| Seq385 | Bacteria | Proteobacteria | Gammaproteobacteria | Salinisphaerales | Solimonadaceae | NA | NA |
$plum \(plum\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]
\(plum\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 17172 0 3034 103 Avg#Reads 490.63
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 27(90%) 16(53.33%) 1(3.33%)
Metadata variables: 3 SampleID, Day, Description
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\(plum\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq161 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | Aquicella | NA |
| Seq181 | Bacteria | Proteobacteria | Gammaproteobacteria | CCD24 | NA | NA | NA |
| Seq207 | Bacteria | Cyanobacteria | Vampirivibrionia | Obscuribacterales | Obscuribacteraceae | NA | NA |
| Seq219 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingomonas | naasensis |
| Seq216 | Bacteria | Proteobacteria | Alphaproteobacteria | Dongiales | Dongiaceae | Dongia | NA |
| Seq220 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | NA |
| Seq90 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Pseudolabrys | NA |
| Seq271 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | NA | NA |
| Seq111 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingobium | NA |
| Seq33 | Bacteria | Proteobacteria | Alphaproteobacteria | Caulobacterales | Caulobacteraceae | Caulobacter | NA |
| Seq189 | Bacteria | Actinobacteriota | Thermoleophilia | Solirubrobacterales | Solirubrobacteraceae | Solirubrobacter | NA |
| Seq85 | Bacteria | Myxococcota | Polyangia | Polyangiales | BIrii41 | NA | NA |
| Seq208 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | Galbitalea | NA |
| Seq218 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | Sphingobacteriaceae | Mucilaginibacter | NA |
| Seq215 | Bacteria | Firmicutes | Bacilli | Bacillales | Bacillaceae | Bacillus | NA |
| Seq177 | Bacteria | Fibrobacterota | Fibrobacteria | Fibrobacterales | Fibrobacteraceae | NA | NA |
| Seq375 | Bacteria | Chloroflexi | Chloroflexia | Thermomicrobiales | JG30-KF-CM45 | NA | NA |
| Seq430 | Bacteria | Planctomycetota | Phycisphaerae | Phycisphaerales | Phycisphaeraceae | NA | NA |
| Seq368 | Bacteria | Planctomycetota | Planctomycetes | Pirellulales | Pirellulaceae | NA | NA |
| Seq152 | Bacteria | Planctomycetota | Planctomycetes | Gemmatales | Gemmataceae | Gemmata | NA |
| Seq304 | Bacteria | Planctomycetota | Planctomycetes | Planctomycetales | NA | NA | NA |
| Seq141 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Terrimonas | NA |
| Seq343 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | NA | NA |
| Seq412 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Edaphobaculum | NA |
| Seq457 | Bacteria | Proteobacteria | Gammaproteobacteria | Coxiellales | Coxiellaceae | Coxiella | NA |
| Seq130 | Bacteria | Proteobacteria | Gammaproteobacteria | R7C24 | NA | NA | NA |
| Seq346 | Bacteria | Proteobacteria | Gammaproteobacteria | Salinisphaerales | Solimonadaceae | Alkanibacter | NA |
| Seq474 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | NA | NA |
| Seq472 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | NA | NA |
| Seq227 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | NA | NA |
$red \(red\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 75 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 75 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 75 tips and 74 internal nodes ] refseq() DNAStringSet: [ 75 reference sequences ]
\(red\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 75 66650 241 5339 1528 Avg#Reads 1904.29
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 75(100%) 75(100%) 75(100%) 74(98.67%) 74(98.67%) 66(88%) 11(14.67%)
Metadata variables: 3 SampleID, Day, Description
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\(red\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq117 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Burkholderiaceae | Burkholderia | NA |
| Seq60 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Alcaligenaceae | NA | NA |
| Seq121 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Comamonadaceae | Variovorax | NA |
| Seq383 | Bacteria | Proteobacteria | Alphaproteobacteria | Ferrovibrionales | Ferrovibrionaceae | Ferrovibrio | soli |
| Seq228 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | NA | NA |
| Seq178 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Beijerinckiaceae | Methylobacterium-Methylorubrum | NA |
| Seq171 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Beijerinckiaceae | Bosea | thiooxidans |
| Seq341 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Beijerinckiaceae | Bosea | NA |
| Seq89 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Tardiphaga | robiniae |
| Seq31 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Xanthobacteraceae | Starkeya | NA |
| Seq160 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Hyphomicrobiaceae | Hyphomicrobium | NA |
| Seq251 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingopyxis | NA |
| Seq373 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Altererythrobacter | NA |
| Seq108 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Mesorhizobium | NA |
| Seq71 | Bacteria | Actinobacteriota | Thermoleophilia | Solirubrobacterales | Solirubrobacteraceae | Conexibacter | NA |
| Seq338 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Pajaroellobacter | NA |
| Seq230 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Pajaroellobacter | NA |
| Seq88 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Sorangium | NA |
| Seq303 | Bacteria | Actinobacteriota | Acidimicrobiia | Microtrichales | Ilumatobacteraceae | NA | NA |
| Seq93 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Promicromonosporaceae | Promicromonospora | NA |
| Seq366 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | Leifsonia | NA |
| Seq134 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | NA | aoyamense |
| Seq411 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | Agromyces | NA |
| Seq115 | Bacteria | Actinobacteriota | Actinobacteria | Corynebacteriales | Mycobacteriaceae | Mycobacterium | NA |
| Seq128 | Bacteria | Actinobacteriota | Actinobacteria | Streptosporangiales | Streptosporangiaceae | Herbidospora | mongoliensis |
| Seq398 | Bacteria | Actinobacteriota | Actinobacteria | Streptosporangiales | Streptosporangiaceae | Nonomuraea | NA |
| Seq78 | Bacteria | Actinobacteriota | Actinobacteria | Streptosporangiales | Thermomonosporaceae | Actinocorallia | NA |
| Seq193 | Bacteria | Actinobacteriota | Actinobacteria | Streptomycetales | Streptomycetaceae | Streptomyces | NA |
| Seq148 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | Sphingobacteriaceae | Pedobacter | NA |
| Seq307 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | NS11-12 marine group | NA | NA |
| Seq431 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | NS11-12 marine group | NA | NA |
| Seq205 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | lautus |
| Seq86 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq51 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq18 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq192 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq266 | Bacteria | Firmicutes | Bacilli | Paenibacillales | Paenibacillaceae | Paenibacillus | NA |
| Seq278 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Domibacillus | NA |
| Seq99 | Bacteria | Firmicutes | Bacilli | Bacillales | Bacillaceae | Bacillus | NA |
| Seq53 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Lysinibacillus | NA |
| Seq118 | Bacteria | Firmicutes | Bacilli | Bacillales | Planococcaceae | Lysinibacillus | NA |
| Seq76 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Terrimicrobiaceae | Terrimicrobium | NA |
| Seq232 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Terrimicrobiaceae | Terrimicrobium | NA |
| Seq168 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Terrimicrobiaceae | Terrimicrobium | NA |
| Seq387 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Chthoniobacteraceae | Chthoniobacter | NA |
| Seq285 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Chthoniobacterales | Chthoniobacteraceae | Chthoniobacter | NA |
| Seq217 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Verrucomicrobiales | Verrucomicrobiaceae | Verrucomicrobium | spinosum |
| Seq190 | Bacteria | Planctomycetota | Planctomycetes | Gemmatales | Gemmataceae | Gemmata | NA |
| Seq249 | Bacteria | Planctomycetota | Planctomycetes | Isosphaerales | Isosphaeraceae | Singulisphaera | NA |
| Seq254 | Bacteria | Acidobacteriota | Acidobacteriae | Acidobacteriales | Acidobacteriaceae (Subgroup 1) | Edaphobacter | NA |
| Seq67 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq176 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq268 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Pseudoflavitalea | NA |
| Seq32 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Pseudoflavitalea | NA |
| Seq84 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Pseudoflavitalea | NA |
| Seq459 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | NA |
| Seq40 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | hibisci |
| Seq173 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | NA |
| Seq246 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | NA |
| Seq112 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Flavitalea | NA |
| Seq126 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | ginsengihumi |
| Seq102 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | arvensicola |
| Seq309 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | soli |
| Seq70 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq262 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq301 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Taibaiella | NA |
| Seq572 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Moraxellaceae | NA | NA |
| Seq436 | Bacteria | Proteobacteria | Gammaproteobacteria | Steroidobacterales | Steroidobacteraceae | Steroidobacter | NA |
| Seq261 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq298 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq354 | Bacteria | Proteobacteria | Gammaproteobacteria | Gammaproteobacteria Incertae Sedis | Unknown Family | Acidibacter | NA |
| Seq226 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Rhodanobacteraceae | Tahibacter | NA |
| Seq147 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Xanthomonas | NA |
| Seq370 | Bacteria | Proteobacteria | Gammaproteobacteria | Diplorickettsiales | Diplorickettsiaceae | NA | NA |
| Seq486 | Bacteria | Proteobacteria | Gammaproteobacteria | NA | NA | NA | NA |
$salmon \(salmon\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 73 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 2 sample variables ] tax_table() Taxonomy Table: [ 73 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 73 tips and 72 internal nodes ] refseq() DNAStringSet: [ 73 reference sequences ]
\(salmon\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 73 115332 0 20534 779 Avg#Reads 3295.2
Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 73(100%) 73(100%) 73(100%) 72(98.63%) 71(97.26%) 66(90.41%) 12(16.44%)
Metadata variables: 3 SampleID, Day, Description
\(salmon\)heat
\(salmon\)heat_rel
\(salmon\)tree
\(salmon\)taxa
| Kingdom | Phylum | Class | Order | Family | Genus | Species | |
|---|---|---|---|---|---|---|---|
| Seq79 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | Massilia | armeniaca |
| Seq122 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | NA | NA |
| Seq179 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | Pseudoduganella | NA |
| Seq145 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | Pseudoduganella | eburnea |
| Seq154 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | Massilia | NA |
| Seq222 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Oxalobacteraceae | Massilia | NA |
| Seq159 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Burkholderiaceae | Cupriavidus | NA |
| Seq8 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Burkholderiaceae | Cupriavidus | NA |
| Seq14 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Alcaligenaceae | Achromobacter | NA |
| Seq54 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Comamonadaceae | NA | paradoxus |
| Seq95 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Comamonadaceae | Xylophilus | NA |
| Seq340 | Bacteria | Proteobacteria | Gammaproteobacteria | Burkholderiales | Comamonadaceae | Rhizobacter | NA |
| Seq264 | Bacteria | Proteobacteria | Alphaproteobacteria | Sphingomonadales | Sphingomonadaceae | Sphingomonas | mucosissima |
| Seq333 | Bacteria | Proteobacteria | Alphaproteobacteria | Reyranellales | Reyranellaceae | Reyranella | NA |
| Seq158 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Beijerinckiaceae | Microvirga | NA |
| Seq248 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Allorhizobium | NA |
| Seq245 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Devosiaceae | Devosia | neptuniae |
| Seq185 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Shinella | NA |
| Seq156 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | NA | NA |
| Seq42 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | NA | NA |
| Seq286 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Ensifer | NA |
| Seq21 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Allorhizobium | NA |
| Seq107 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Neorhizobium | NA |
| Seq231 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | Allorhizobium | azooxidifex |
| Seq140 | Bacteria | Proteobacteria | Alphaproteobacteria | Rhizobiales | Rhizobiaceae | NA | NA |
| Seq378 | Bacteria | Proteobacteria | Alphaproteobacteria | Caulobacterales | Caulobacteraceae | Phenylobacterium | mobile |
| Seq374 | Bacteria | Myxococcota | Polyangia | Haliangiales | Haliangiaceae | Haliangium | NA |
| Seq257 | Bacteria | Myxococcota | Polyangia | Polyangiales | Polyangiaceae | Pajaroellobacter | NA |
| Seq223 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Promicromonosporaceae | Cellulosimicrobium | NA |
| Seq83 | Bacteria | Actinobacteriota | Actinobacteria | Micrococcales | Microbacteriaceae | Microbacterium | NA |
| Seq68 | Bacteria | Actinobacteriota | Actinobacteria | Corynebacteriales | Mycobacteriaceae | Mycobacterium | NA |
| Seq293 | Bacteria | Actinobacteriota | Actinobacteria | Glycomycetales | Glycomycetaceae | Glycomyces | NA |
| Seq72 | Bacteria | Actinobacteriota | Actinobacteria | Streptomycetales | Streptomycetaceae | Streptomyces | NA |
| Seq101 | Bacteria | Actinobacteriota | Actinobacteria | Streptomycetales | Streptomycetaceae | Streptomyces | NA |
| Seq265 | Bacteria | Actinobacteriota | Actinobacteria | Streptomycetales | Streptomycetaceae | Streptomyces | NA |
| Seq260 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | NA | NA | NA |
| Seq180 | Bacteria | Bacteroidota | Bacteroidia | Sphingobacteriales | Sphingobacteriaceae | Pedobacter | panaciterrae |
| Seq142 | Bacteria | Verrucomicrobiota | Verrucomicrobiae | Verrucomicrobiales | Verrucomicrobiaceae | Roseimicrobium | NA |
| Seq163 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq253 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq116 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq184 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Microscillaceae | Ohtaekwangia | NA |
| Seq52 | Bacteria | Bacteroidota | Bacteroidia | Flavobacteriales | Flavobacteriaceae | Flavobacterium | NA |
| Seq187 | Bacteria | Bacteroidota | Bacteroidia | Flavobacteriales | Weeksellaceae | Chryseobacterium | ginsenosidimutans |
| Seq172 | Bacteria | Bacteroidota | Bacteroidia | Flavobacteriales | Weeksellaceae | Chryseobacterium | NA |
| Seq283 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Flavitalea | NA |
| Seq113 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | NA |
| Seq110 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Niastella | NA |
| Seq132 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Pseudoflavitalea | NA |
| Seq37 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq162 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq182 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | humicola |
| Seq92 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq80 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | pinensis |
| Seq2 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq221 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq20 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq282 | Bacteria | Bacteroidota | Bacteroidia | Chitinophagales | Chitinophagaceae | Chitinophaga | NA |
| Seq38 | Bacteria | Bacteroidota | Bacteroidia | Cytophagales | Spirosomaceae | Dyadobacter | NA |
| Seq237 | Bacteria | Proteobacteria | Gammaproteobacteria | Steroidobacterales | Steroidobacteraceae | Steroidobacter | agariperforans |
| Seq234 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Pseudoxanthomonas | NA |
| Seq59 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Stenotrophomonas | NA |
| Seq105 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Stenotrophomonas | NA |
| Seq344 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Lysobacter | NA |
| Seq41 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Lysobacter | NA |
| Seq243 | Bacteria | Proteobacteria | Gammaproteobacteria | NA | NA | NA | NA |
| Seq406 | Bacteria | Proteobacteria | Gammaproteobacteria | Legionellales | Legionellaceae | Legionella | NA |
| Seq139 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Pseudomonadaceae | Pseudomonas | NA |
| Seq24 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Pseudomonadaceae | Pseudomonas | NA |
| Seq27 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Pseudomonadaceae | Pseudomonas | NA |
| Seq87 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Pseudomonadaceae | Pseudomonas | NA |
| Seq55 | Bacteria | Proteobacteria | Gammaproteobacteria | Pseudomonadales | Pseudomonadaceae | Pseudomonas | NA |
| Seq201 | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Klebsiella | NA |